I'm an avid user of the Goodreader App, and had an extensive iCloud library of files on iCloud that I used for work. The second I upgraded to iCloud drive on my 6+ everything is gone, and iCloud sync doesn't work anymore. I have the same issue after installing the Goodreader update that uses iCloud drive.
It seems that everything I had stored (20gb of files) pre iOS 8 is gone. How can this be?!?!
Apple has really let me down lately on the software and cloud services categories.
Take a look at the three Readdle apps, Documents, PDF Expert and Scanner pro.
I think they are ahead of the field at the moment, but I think this is a fast moving area, and may not be true for long.
Readdle creates a folder on the iCloud Drive, which can hold any type of file. The same folder appears in iCloud Drive and on the iPhone, with contents sync'd. You can add files on the Mac or the iPhone.
PDF Expert can open (at least) Pages, Numbers PDF docs on the iPhone by converting them to PDF. Not tried docx and xlsx but would be surprised if not.
Not perfect, but I think ahead of the game at the moment.